The phylogeny of the Human Immunodeficiency Virus type 1 (HIV-1) is characterized by extensive diversity. However when it comes to the persistence of the virus not all of this diversity is relevant. In this thesis I show that the significance of diversity, both In relation to epidemiology and vaccine design, varies within and between the HIV-1 groups. The substructure present within group O and at the center of the group M pandemic was observed to be similar to that found on random tree topologies, whereas the substructure present within globally sampled group M strains was significantly different.